Abstract
CRISPR-Cas systems are diverse, with microbes harboring multiple classes and subtypes. Type I DNA-targeting and type III RNA-targeting systems often co-occur, but their interactions remain unclear. Prodigiosinella has three CRISPR-Cas systems (I-E, I-F, and III-A) with independent adaptation machinery. Type III systems can trigger cell death, yet it is unknown how functional spacers are acquired. We found that type I interference generates substrates acquired by the type III adaptation machinery. Despite reducing type I interference efficiency, type III contributed to plasmid loss and provided an advantage when DNA-targeting systems failed. Type I priming influenced type III spacer length and source, with more spacers acquired near the type I target site. Invader DNA clearance by type I interference enabled retention of cytotoxic type III spacers that would otherwise be lost. This study reveals how RNA-targeting CRISPR-Cas systems function as a backup in multi-system hosts, bolstering population-level protection.